1 Rescaling and Filtering

Significant genes in tumor-only
Because I didn’t use COSMIC VCF fils (COSMIC.CNT) for PureCN run, many SNVs in dbSNP were removed in the prior.somatic filtering process. Here, as a ‘quick and dirty’ fix, we tried rescaling (~/data2/PureCN_manuscript/Revision/dNdSCV/script/rescale_priors.R).

2 Summary Table

2.1 All the significant genes

Passed the FDR < 0.01 from tumor-only or mathing-normal analyses.

##           Gene Matching normal   Tumor only
## 8957      KRAS    0.000000e+00 0.000000e+00
## 17832     TP53    0.000000e+00 0.000000e+00
## 8720     KEAP1    8.261399e-08 1.295550e-03
## 1646    ATF7IP    7.326080e-05 1.217567e-03
## 1447    ARID1A    1.002786e-04 2.714297e-04
## 16557    STK11    1.581153e-04 2.667679e-03
## 2097      BRAF    1.357334e-03 4.399990e-02
## 14094      RB1    8.750807e-03 2.295630e-01
## 3782     CMTR2    8.918358e-03 9.999985e-01
## 11993    OR5F1    9.221523e-03 3.513581e-03
## 15904  SMARCA4    9.221523e-03 3.978034e-01
## 11988   OR5D13    1.171696e-02 1.217567e-03
## 11808   OR2AK2    4.774436e-02 4.341506e-03
## 3134      CD8B    9.999998e-01 0.000000e+00
## 3978     COX10    9.999998e-01 0.000000e+00
## 7620  HLA-DRB1    9.999998e-01 0.000000e+00
## 8129  IGLV5-48    9.999998e-01 0.000000e+00
## 8818   KIR2DL3    9.999998e-01 0.000000e+00
## 8821   KIR3DL2    9.999998e-01 0.000000e+00
## 9338    LILRB3    9.999998e-01 1.813283e-03
## 13147   POLRMT    9.999998e-01 1.217567e-03
## 13366 PRAMEF18    9.999998e-01 0.000000e+00
## 13587    PRSS3    9.999998e-01 3.301081e-07
## 14157   RBMXL1    9.999998e-01 2.119224e-08
## 17096      TEK    9.999998e-01 2.860557e-08
## 17934  TRAPPC4    9.999998e-01 6.296753e-06

2.2 Mutually called significant genes

Passed the FDR < 0.01 from both tumor-only and mathing-normal analyses.

##   gene_name qglobal_cv_tumorOnly qglobal_cv_matchingN
## 1      KRAS         0.0000000000         0.000000e+00
## 2      TP53         0.0000000000         0.000000e+00
## 3    ARID1A         0.0002714297         1.002786e-04
## 4    OR5D13         0.0012175668         1.171696e-02
## 5    ATF7IP         0.0012175668         7.326080e-05
## 6     KEAP1         0.0012955505         8.261399e-08
## 7     STK11         0.0026676788         1.581153e-04
## 8     OR5F1         0.0035135813         9.221523e-03
## 9    OR2AK2         0.0043415063         4.774436e-02

3 Venn Diagram

## (polygon[GRID.polygon.1], polygon[GRID.polygon.2], polygon[GRID.polygon.3], polygon[GRID.polygon.4], text[GRID.text.5], text[GRID.text.6], text[GRID.text.7], text[GRID.text.8], text[GRID.text.9])

4 Cancer Genes